SUMMARY The fossil record is incomplete, so molecular divergence time analysis is a crucial tool in estimating evolutionary timescales. MCMCtree contained in the PAML software provides Bayesian methods to estimate divergence times of genomic-sized sequences. Here, I present MCMCtreeR, a flexible R package to prepare time priors for MCMCtree analysis and plot time-scaled phylogenies. The package provides functions to refine parameters and visualize time-calibrated node prior distributions so that these priors accurately reflect confidence in known, usually fossil, time information. After the parameters have been chosen, the package produces output files ready for MCMCtree analysis. Following analysis, the package has tools to compare prior and posterior calibrated node age distributions and produce plots of the time-scaled phylogenies. The plotting functions allow for the inclusion of age uncertainty on time-scaled phylogenies, including the display of full posterior distributions on nodes. Options also allow for the inclusion of the geological timescale, and these plotting functions are applicable with posterior age estimates from any Bayesian divergence time estimation software. AVAILABILITY AND IMPLEMENTATION MCMCtreeR is an R package available on CRAN (https://CRAN.R-project.org/package=MCMCtreeR). MCMCtreeR depends on the R packages ape, sn and stats4.

中文翻译：

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MCMCtreeR：用于准备MCMCtree分析并可视化树木的后龄的功能。

总结化石记录是不完整的，因此分子发散时间分析是估计进化时间尺度的关键工具。PAML软件中包含的MCMCtree提供了贝叶斯方法来估计基因组大小序列的发散时间。在这里，我介绍了MCMCtreeR，这是一个灵活的R包，可以为MCMCtree分析准备时间先验并绘制时间标度的系统发育图。该软件包提供了一些功能，可以优化参数并可视化时间校准的节点先验分布，从而使这些先验准确地反映出对已知（通常是化石）时间信息的信心。选择参数后，程序包将生成输出文件，准备进行MCMCtree分析。经过分析后，该软件包提供了一些工具，可以比较之前和之后校准的节点年龄分布，并生成时间标度的系统发育图。绘图功能允许将年龄不确定性包括在时间标度的系统发育中，包括在节点上显示全部后验分布。选项还允许包括地质时标，并且这些绘图功能适用于任何贝叶斯发散时间估计软件的后验年龄估计。可用性和实现MCMCtreeR是R软件包，可在CRAN（https://CRAN.R-project.org/package=MCMCtreeR）上获得。MCMCtreeR取决于R包ape，sn和stats4。并且这些绘图功能适用于任何贝叶斯发散时间估计软件中的后验年龄估计。可用性和实现MCMCtreeR是R软件包，可在CRAN（https://CRAN.R-project.org/package=MCMCtreeR）上获得。MCMCtreeR取决于R包ape，sn和stats4。并且这些绘图功能适用于任何贝叶斯发散时间估计软件中的后验年龄估计。可用性和实现MCMCtreeR是R软件包，可在CRAN（https://CRAN.R-project.org/package=MCMCtreeR）上获得。MCMCtreeR取决于R包ape，sn和stats4。